Relaxed potential energy surfaces of N‐linked oligosaccharides: The mannose‐α(1 → 3)‐mannose case

Abstract

We report calculations of potential energy surfaces where all the internal coordinates of the disaccharide M a n 4 1 + 3)-Man-a-O-Me were relaxed and minimized through an extensive molecular mechanics scheme. Flexibility within the mannopyranose rings plays a crucial role. Introduction of the relaxed principle into the conformational description of the disaccharide does not greatly alter the overall shape of the low-energy domains but it reveals new local minima. However, its principle effect is the lowering of energy barriers in the potential energy surface. New conformational transitions about the glycosidic bonds appear, permiting pathways among the low energy sections. This occurs with only little variation of the classical 4C1 conformation of the mannopyranose residues. All the conformations observed in the solid state, along with those already predicted through the joint use of NMR and modeling techniques, fall into the populations of stable conformers calculated in the present work. Moreover, a satisfactory agreement is reached between previously observed NOE values, and the theoretical one, calculated from the averaging of more than 500 microstates. The present results reconciliate most of the apparently conflicting data previously reported; they provide strong support for the application of the concept of conformational averaging to solution behavior. Some limitations of the proposed methodology are also discussed.

The potential energy surface of methyl 3‐O‐(α‐D‐mannopyranosyl)‐α‐D‐mannopyranoside in aqueous solution: Conclusions derived from optical rotation

“…A rigid residue modeling with the Momany-Scheraga nonbonded potential, which leads to population of the A and C regions, is approximately consistent with the optical rotation, but apparently misses the B region that, later flexible residue calculations indicate, provides the major pathway for A-C conversions. All flexible residue modeling calculations, by simple inspection of the resulting potential energy surfaces, [24][25][26] appear to be qualitatively compatible with the optical rotation inasmuch as they indicate a major population of the A and B regions with a smaller, yet significant, population of the C region.…”

mm3 Potential energy surfaces of α-3-linked l-fucobiose and fucotriose and their sulfated counterparts

“…In order to proceed with NOE theoretical calculations, the average matrix of H-H distances was obtained from the statistical population of the minima as shown by Imberty et al 24 Once this matrix was obtained, the NOEs were computed by an iterative procedure 25 and expressed as increases in 1 H NMR peak intensity when irradiating the anomeric proton, relative to the NOE on its neighboring proton H-2.…”

Structural Basis of the Preferential Binding for Globo-Series Glycosphingolipids Displayed by Pseudomonas aeruginosa Lectin I

“…27 This so-called flexible energy map of the αGal1-3Gal linkage has been previously calculated in our group. 28 The αGal1-4Gal linkage was calculated using the same approach.…”